Hi AMBER community,
I'm curious if a group-based cutoff can be implemented with the AMBER
force fields (I'm looking at all_amino02.lib in particular). It seems
that when I try to group atoms together in alanine, for example, I can't
make charge neutral groups. Are non-neutral groups used? Is a
residue-based cutoff used at all or is it done based on atom-atom distances?
Sorry for any redundancy, but couldn't find much in the manual or
archive about this. Thank you for your time,
John Vieceli
--
John S. Vieceli, Ph.D.
Molecular Simulations Lead
Zymeworks, Inc.
201-1401 W. Broadway Ave.
Vancouver, B.C. Canada V6H 1H6
t: (604) 678-1388 x25
f: (604) 737-7077
www.zymeworks.com
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Received on Thu Aug 11 2005 - 01:53:00 PDT
